Witold Filipowicz - Major Publications#

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1. Filipowicz, W., Sierra, J.M. and Ochoa, S. Polypeptide chain initiation in eukaryotes: Initiation factor MP in Artemia salina embryos. Proc. Natl. Acad. Sci. USA 72, 3947 3951 (1975).

2. Muthukrishnan, S., Filipowicz, W., Sierra, J.M., Both, G.W., Shatkin, A.J. and Ochoa, S. mRNA methylation and protein synthesis in extracts from embryos of brine shrimp Artemia salina. J. Biol. Chem. 250, 9336 9341 (1975).

3. Filipowicz, W., Sierra, J.M., Nombela, C., Ochoa, S., Merrick, W.C. and Anderson, W.F. Polypeptide chain initiation in eucaryotes: Initiation factor requirements for translation of natural messengers. Proc. Natl. Acad. Sci. USA 73, 44 48 (1976).

4. Filipowicz, W., Furuichi, Y., Sierra, J.M., Muthukrishnan, S., Shatkin, A.J. and Ochoa, S. A protein binding the methylated 5' terminal cap, m7GpppN, of eukaryotic messenger RNA. Proc. Natl. Acad. Sci. USA 73, 1559 1563 (1976).

5. Zan Kowalczewska, M., Bretner, M., Sierakowska, H., Szczesna, E., Filipowicz, W. and Shatkin, A.J. Removal of 5' terminal m7G from eukaryotic mRNAs by potato nucleotide pyrophosphatase and its effect on translation. Nucl. Acids Res. 4, 3065 3081 (1977).

6. Wodnar Filipowicz, A., Szczesna, E., Zan Kowalczewska, M., Muthukrishnan, S., Szybiak, U., Legocki, A.B. and Filipowicz, W. 5' terminal 7 methylguanosine and mRNA function: The effect of enzymatic decapping and of cap analogs on in vitro translation of TMV RNA and globin mRNA. Eur. J. Biochem. 92, 69 80 (1978).

7. Filipowicz, W. and Haenni, A.L. Binding of ribosomes to 5' terminal leader sequences of eukaryotic messenger RNAs. Proc. Natl. Acad. Sci. USA 76, 3111 3115 (1979).

8. Konarska, M., Filipowicz, W., Domdey, H. and Gross, H.J. Formation of a 2' phosphomonoester, 3', 5' phosphodiester linkage by a novel RNA ligase in wheat germ. Nature 293, 112 116 (1981).

9. Konarska, M., Filipowicz, W. and Gross, H.J. RNA ligation via 2' phosphomonoester,3', 5' phosphodiester linkage: Requirement of 2,3' cyclic phosphate termini and involvement of a 5' hydroxyl polynucleotide kinase. Proc. Natl. Acad. Sci. USA 79, 1474 1478 (1982).

10. Filipowicz, W. and Shatkin, A.J. Origin of splice junction phosphate in tRNAs processed by HeLa cell extract. Cell 32, 547 557 (1983).

11. Filipowicz, W., Konarska, M., Gross, H.J. and Shatkin, A.J. RNA 3' terminal phosphate cyclase activity and RNA ligation in HeLa cell extract. Nucl. Acids Res. 11, 1405 1418 (1983).

12. Filipowicz, W., Strugala, K., Konarska, M. and Shatkin, A.J. Cyclisation of RNA 3' terminal phosphate by cyclase from HeLa cells proceeds via formation of N(3')pp(5')A activated intermediate. Proc. Natl. Acad. Sci. USA 82, 1316 1320 (1985).

13. Genschik, P., Billy, E., Swianiewicz, M. and Filipowicz, W. The human RNA 3'-terminal phosphate cyclase is a member of a new family of proteins conserved in Eucarya, Bacteria and Archaea. EMBO J., 16, 2955-2967 (1997).

14. Genschik, P., Drabikowski, K. and Filipowicz, W. Characterization of the Escherichia coli RNA 3'-terminal phosphate cyclase and its σ54-regulated operon. J. Biol. Chem. 273, 25516-25526 (1998).

15. Palm, G.J., Billy, E., Filipowicz, W. and Wlodawer A. Crystal structure of RNA 3'-terminal phosphate cyclase, a ubiquitous enzyme with unusual topology. Structure, 8, 13-23 (2000).

16. Billy, E., Wegierski, T., Nasr, F. and Filipowicz, W. Rcl1p, the yeast protein similar to the RNA 3’-phosphate cyclase, associates with U3 snoRNP and is required for 18S rRNA biogenesis. EMBO J. 19, 2115-2126 (2000).

17. Wiebauer, K., Herrero, J.J., Filipowicz, W. Nuclear pre mRNA splicing in plants: distinct modes of 3' splice site recognition in plants and animals. Mol. Cell. Biol. 8, 2042 2051 (1988).

18. Goodall, G. and Filipowicz, W. The AU rich sequences present in introns of plant nuclear pre mRNAs are required for splicing. Cell 58, 473 483 (1989).

19. Goodall, G. and Filipowicz, W. Different effects of intron nucleotide composition and secondary structure on pre mRNA splicing in monocot and dicot plants. EMBO J. 10, 2635 2644 (1991).

20. Liu, H.X., Goodall, G., Kole, R. and Filipowicz, W. Effects of secondary structure on pre-mRNA splicing: Hairpins sequestering the 5' but not the 3' splice site inhibit intron processing in Nicotiana plumbaginifolia. EMBO J., 14, 377-388 (1995).

21. Kiss, T. and Filipowicz, W. Evidence against a mitochondrial location of the 7 2/MRP RNA in mammalian cells. Cell 70, 11 16 (1992).

22. Kiss, T., Marshallsay, C. and Filipowicz, W. 7 2/MRP RNAs in plant and mammalian cells: Association with higher order structures in the nucleolus. EMBO J.11, 3737 3746 (1992).

23. Shimba, S., Buckley, B., Reddy, R., Kiss, T. and Filipowicz, W. Cap structure of U3 small nucleolar RNA in animal and plant cells is different: gamma monomethyl phosphate cap structure in plant RNA. J. Biol. Chem. 267, 13772 13777 (1992).

24. Kiss, T. and Filipowicz, W. Small nucleolar RNAs encoded by introns of the human cell cycle regulatory gene RCC1. EMBO J. 12, 2913-2920 (1993).

25. Kiss, T. and Filipowicz, W. Exonucleolytic processing of small nucleolar RNAs from pre-mRNA introns. Genes Dev. 9, 1411-1424 (1995).

26. Dragon, F., Pogacic, V. and Filipowicz, W. In vitro assembly of human H/ACA small nucleolar RNPs reveals unique features of U17 and telomerase RNAs. Mol. Cell. Biol. 20, 3037-3048 (2000).

27. Waibel, F. and Filipowicz, W. Determination of RNA polymerase specificity of transcription of Arabidopsis U snRNA genes by promoter element spacing. Nature 346, 199 202 (1990).

28. Kiss, T., Marshallsay, C. and Filipowicz, W. Alteration of the RNA polymerase specificity of U3 snRNA genes during evolution and in vitro. Cell 65, 517 526 (1991).

29. Waibel, F. and Filipowicz, W. U6 snRNA genes of Arabidopsis are transcribed by RNA polymerase III but contain the same two upstream promoter elements as RNA polymerase II transcribed U snRNA genes. Nucl. Acids Res. 18, 3459 3466 (1990).

30. Vankan, P. and Filipowicz, W. A U snRNA gene specific upstream element and a 30 "TATA box" are required for transcription of the U2 snRNA gene of Arabidopsis thaliana. EMBO J. 8, 3875 3882 (1989).

31. Zhang, H., Kolb, F. A., Jaskiewicz, L., Westhof, E. Filipowicz, W. Single processing center models for human Dicer and bacterial RNase III. Cell 118, 57-68. (2004)

32. Zhang H, Kolb FA, Brondani V, Billy E and Filipowicz W. (2002) Human Dicer preferentially cleaves dsRNAs at their termini without a requirement for ATP. EMBO J. 21, 5875-5885.

33. Pillai, R., Bhattacharyya, S., Artus, C., Zoller, T., Cougot, N., Basyuk, E., Bertrand, E., and Filipowicz, W. Inhibition of translational initiation by let-7 microRNA in human cells. Science. 309:1573-6 (2005).

34. Filipowicz, W. RNAi: The nuts and bolts of the RISC machine. Cell 122, 17-20 (2005).

35. Bhattacharyya S, Habermacher R, Martine U, Closs EI and Filipowicz W. Relief of microRNA-mediated translational repression in human cells subjected to stress. Cell 125, 1111 – 1124 (2006).

36. Mathonnet G. Fabian MR. Svitkin YV. Parsyan A. Huck L. Murata T. Biffo S. Merrick WC. Darzynkiewicz E. Pilai R. Filipowicz W. Duchaine TF. Sonenberg N (2007). MicroRNA inhibition of translation initiation in vitro by targeting the cap-binding complex elF4F. Science 317, 1764-1767.

37. Sinkkonen L. Hugenschmidt T. Berninger P. Gaidatzis D. Mohn F. Artus-Revel C. Zavolan M. Svoboda P. Filipowicz W. (2008) MicroRNAs control de novo DNA methylation through regulation of transcriptional repressors in mouse embryonic stem cells. (2008) Nature Str. Mol. Biol. 15, 259-267.

38. Filipowicz W. Bhattacharyya SN. Sonenberg N. (2008) Mechanisms of post-transcriptional regulation by microRNAs: Are the answers in sight? Nature Rev. Gen. 9, 102-114.

39. Sarasin-Filipowicz M, Krol J, Markiewicz I, Heim M and Filipowicz W. (2009) Decreased levels of microRNA miR-122 in hepatitis C patients with poor response to interferon therapy. Nature Medicine 15:31-33.

40. Trabucchi M, Briata P, Garcia-Mayoral M, Haase AD, Filipowicz W, Ramos A, Gherzi R and Rosenfeld MG. (2009) The RNA-binding protein KSRP Promotes the Biogenesis of a Subset of miRNAs. Nature 459, 1010-1014.

41. Fabian MR, Mathonnet G, Sundermeier T, Mathys H, Zipprich JT, Svitkin YV, Rivas F, Jinek M, Wohlschlegel J, Doudna JA, Chen CA, Shyu AB, Yates III JR, Hannon GJ, Filipowicz W, Duchaine TF, Sonenberg N. (2009) Mammalian miRNA RISC recruits CAF1 and PABP to effect PABP-dependent deadenylation. Mol. Cell 35, 868-80.

42. Krol J, Busskamp V, Markiewicz I, Stadler MB, Ribi S, Richter J, Duebel J, Bicker S, Fehling HJ, Schübeler D, Oertner TG, Schratt G, Bibel M, Roska B & Filipowicz W (2010) Characterization of microRNAs induced by light adaptation in mouse retina reveals rapid turnover as a common property of neuronal microRNAs. Cell 141:618-31.

43. Fabian M.R., Sonenberg N. and Filipowicz W. (2010). Regulation of mRNA translation and stability by microRNAs. Annual Review of Biochemistry, 79:351-79.

44. Krol J, Loedige I and Filipowicz W (2011) Regulation of miRNA Biogenesis, Function and Decay, Nature Reviews Genetics 11, 597-615.

45. Chekulaeva M, Mathys H, Zipprich JT, Attig J, Colic M, Parker R, Filipowicz W. (2011) MicroRNA repression involves GW182-mediated recruitment of CCR4-NOT through conserved W-containing motifs. Nat Struct Mol Biol. 18:1218-26.

46. Bethune J, Artus-Revel C, and Filipowicz W. (2012) Kinetic analysis reveals successive steps leading to miRNA-mediated silencing in mammalian cells. EMBO Reports, 13(8): 716-23.

47. Doyle M, Badertscher L, Jaskiewicz L, Güttinger S, Jurado S, Hugenschmidt T, Kutay U, Filipowicz W. (2013) The double-stranded RNA binding domain of human Dicer functions as a nuclear localization signal. RNA 19(9): 1238-52.

48. Loedige I, Gaidatzis D, Sack R, Meister G, Filipowicz W. (2013). The mammalian TRIM-NHL protein TRIM71/LIN-41 is a repressor of mRNA function. Nucleic Acids Res. 41(1): 518-32.

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